This task is devoted to introduce GROMACS notation for force fields. We build the model of hydrazine molecule, introducing lone electron pair as an artificial atom. We set molecular conformations with pairs or by defining dihedral potential. Varying dihedral potentials or pairs we obtain different equilibrium conformations of hydrazine.
MD Practice #1 — making toy force field
Published in Октябрь 4th, 2018
Posted by comcon1 in Без рубрики
1 Comment
Теория молекулярно-динамических расчетов (видео)
Published in Декабрь 16th, 2016
Posted by comcon1 in Без рубрики
В данном материале публикуется указатель на видеозаписи первой версии теоретической части курса «Теория и практика молекулярно-динамических расчетов», прочитанного А. Нестеренко и Д. Зленко для магистрантов 2го года кафедры биофизики биологического факультета МГУ. В курсе излагаются теоретические основы проведения и обработки молекулярно-динамических расчетов. Материал достаточно сложный и не рекомендуется тем, кто хочет ознакомиться с тем, что […]
Малый практикум по квантовой химии
Published in Май 24th, 2016
Posted by comcon1 in Без рубрики
Малый практикум по квантовой химии проводится для студентов-биофизиков 3го курса и других желающих. Ведущие: Алексей Нестеренко и Дмитрий Зленко. Место проведения: компьютерный класс корпуса ЛИК (Ленинские горы 1, корп. 12). Даты: 26-30 июня 2017 года Практикум призван обучить азам квантовой химии с нуля. Примерная программа: Работа в командной строке linux Работа в PyMOL: визуализация и редактирование молекулярных структур […]
Compiling CP2K
Published in Май 5th, 2016
Posted by Михаил Степанов in Без рубрики
Everyone who deals with CP2K applications faces the problem of their compilation which appears to be rather challenging. Several available guides propose different compilation instructions but the choice of the best one is not evident. Here we provide a guide that would allow you to develop your own CP2K build protocol.
OPLS-AA patch for different types of molecules
Published in Февраль 8th, 2016
Posted by comcon1 in Без рубрики
ERG group members work with different types of molecules and consequently added new atomtypes into classical OPLS-AA distributed with GROMACS. Now the ERG patch of OPLS-AA force field is published at bitbucket as a repository.
Reaction-diffusion systems in 2D space with python
Published in Январь 26th, 2016
Posted by comcon1 in Без рубрики
In our previous article about construction of the discrete Laplacian with numpy we discuss the discrete Laplacian calculation for numerical solving of diffusion PDE. Here we generalize this technique for the two-dimensional space. We describe the complete algorithm of solving of reaction-diffusion equations with implementation of Crank-Nicolson scheme for diffusion part together with Runge-Kutta scheme for […]
Constructing discrete Laplacian via sparse matrix
Published in Январь 24th, 2016
Posted by comcon1 in Без рубрики
In this article we consider calculation of discrete Laplacian for 1D arrays using python/numpy/scipy. We introduce the sparse matrix technique that is rather efficient for computation of certain types of diffusion PDE.
All-atom automatic OPLS-AA topology generator
Published in Май 30th, 2015
Posted by comcon1 in Без рубрики
OPLS-AA topology generation is a very complex task because of huge amount of the atomtypes described this force field. The OPLS-AA force filed contains more than 800 atom types that is nevertheless not sufficient for describing all the diversity of chemical structures. Thus, as parameters for new chemical fragments appears in literature the atomtype database […]
Scanning PES ab initio and in MM
Published in Май 19th, 2015
Posted by comcon1 in Без рубрики
Here is the tutorial about how to scan potential energy over specific internal coordinate (e.g. dihedral angle) ab initio and then transfer this trajectory into molecular mechanics package and compare them.
Quantum chemistry information page
Published in Май 19th, 2015
Posted by comcon1 in Без рубрики
On this page we collect references to our resources, documentation and resources on other sites. All these data are very helpful for everybody who wants to learn practical quantum chemistry.
Метки
Последние записи
- MD Practice #1 — making toy force field
- Теория молекулярно-динамических расчетов (видео)
- Малый практикум по квантовой химии
- Compiling CP2K
- OPLS-AA patch for different types of molecules
- Reaction-diffusion systems in 2D space with python
- Constructing discrete Laplacian via sparse matrix
- All-atom automatic OPLS-AA topology generator
- Scanning PES ab initio and in MM
- Quantum chemistry information page
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